AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene77628

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77628.t1 MTR_1g085720 75.714 70 17 0 1 70 34 103 7.44e-33 117
MS.gene77628.t1 MTR_4g055725 32.941 170 93 4 3 172 110 258 1.02e-20 90.1
MS.gene77628.t1 MTR_4g117120 33.962 106 64 2 1 106 183 282 3.19e-13 70.1
MS.gene77628.t1 MTR_8g073195 35.238 105 65 2 205 309 43 144 4.72e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene77628.t1 AT1G43722 42.081 221 121 3 5 219 100 319 1.71e-56 186
MS.gene77628.t1 AT5G41980 30.719 306 185 6 7 305 78 363 9.02e-47 162
MS.gene77628.t1 AT3G30525 39.623 159 90 2 84 237 1 158 4.47e-35 125
MS.gene77628.t1 AT5G28730 33.702 181 94 3 5 184 58 213 1.57e-31 119
MS.gene77628.t1 AT5G35695 37.226 137 73 2 121 256 24 148 1.38e-25 102
MS.gene77628.t1 AT5G28950 41.758 91 53 0 63 153 8 98 5.14e-22 90.5
MS.gene77628.t1 AT4G10890 42.857 91 51 1 133 223 71 160 4.49e-18 85.1
MS.gene77628.t1 AT4G10890 42.857 91 51 1 133 223 71 160 4.49e-18 85.1
MS.gene77628.t1 AT4G10890 42.857 91 51 1 133 223 71 160 4.49e-18 85.1
MS.gene77628.t1 AT3G55350 25.000 244 148 10 64 287 164 392 7.03e-11 63.2

Find 53 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCTATCATCCTTGATTT+TGG 0.117739 2.3:+29922402 None:intergenic
AGAAATGTTCAAAATAAATT+TGG 0.175729 2.3:-29922535 MS.gene77628:CDS
TTCTTTCAATGACATTTCTA+AGG 0.228551 2.3:+29921870 None:intergenic
TCAAGGATGATAGAAGATTT+TGG 0.248117 2.3:-29922396 MS.gene77628:CDS
CAAAATAAATTTGGAAAATC+AGG 0.272245 2.3:-29922526 MS.gene77628:CDS
AAAGATCAAATTCGTTATAT+TGG 0.275852 2.3:-29922310 MS.gene77628:CDS
GATAGATATCCTTTCATGTT+TGG 0.305736 2.3:+29921986 None:intergenic
AGGCACTTGTGATGTTTCTT+TGG 0.313453 2.3:-29922582 MS.gene77628:CDS
CGAGCATATATCCTTGGATT+TGG 0.329097 2.3:+29921696 None:intergenic
TTTGTTGTTGTTGGCTGGCC+TGG 0.350368 2.3:-29922226 MS.gene77628:CDS
TCTTGTTTGATTAGTGGAAA+TGG 0.370259 2.3:+29921800 None:intergenic
CCGATGCATCCATCAAAATA+AGG 0.371291 2.3:+29922373 None:intergenic
TTGAAAGAACAATTGGTGTT+TGG 0.373420 2.3:-29921856 MS.gene77628:CDS
TAACGAATTTGATCTTTAGT+AGG 0.379665 2.3:+29922316 None:intergenic
TCAAATTGCCACTAAGTTGT+TGG 0.387811 2.3:-29921585 MS.gene77628:CDS
ATTCGTTATATTGGCAGAAA+AGG 0.394672 2.3:-29922301 MS.gene77628:CDS
CTCGTTCGAGCATATATCCT+TGG 0.409241 2.3:+29921690 None:intergenic
AATGTCATTGAAAGAACAAT+TGG 0.424218 2.3:-29921863 MS.gene77628:CDS
GGATGCATCGGTGCTATAGA+TGG 0.439485 2.3:-29922361 MS.gene77628:CDS
AAGATGAGGAATTCAACAAA+TGG 0.440124 2.3:-29921721 MS.gene77628:CDS
TTCACTAAACTTCCTACTTA+CGG 0.442099 2.3:+29922498 None:intergenic
TGACTGCCATCTCTAAAATC+AGG 0.452335 2.3:+29921935 None:intergenic
CAATTGGTGTTTGGAAGAAA+AGG 0.453010 2.3:-29921847 MS.gene77628:CDS
TGATATCTTTCACCTTTGTA+TGG 0.453127 2.3:+29921962 None:intergenic
ATTTCTGTGAAGTTAAAATC+AGG 0.454308 2.3:+29922430 None:intergenic
AAGTATTACTTGGTTGATGC+AGG 0.461050 2.3:-29922013 MS.gene77628:CDS
CATAACTTCATTCGAATATG+TGG 0.472793 2.3:-29921749 MS.gene77628:CDS
CGTGTGTCATGCGCAGTACC+AGG 0.480441 2.3:+29922208 None:intergenic
ATTTCTAGGAAAGTATTACT+TGG 0.498326 2.3:-29922023 MS.gene77628:intron
AGAAATTCCATCCAAAATCA+AGG 0.500971 2.3:-29922413 MS.gene77628:CDS
ATCAAACGAAATGACATCCT+TGG 0.510213 2.3:-29922605 None:intergenic
ATCGTACCTTCAGGAGGATG+AGG 0.518203 2.3:+29922145 None:intergenic
AGATGAGGAATTCAACAAAT+GGG 0.524003 2.3:-29921720 MS.gene77628:CDS
TCTTTCAATGACATTTCTAA+GGG 0.531707 2.3:+29921871 None:intergenic
TATAATTTAAGAGTACAAGA+TGG 0.540136 2.3:-29921632 MS.gene77628:CDS
TCTTTAGTAGGAACGATGGC+AGG 0.548988 2.3:+29922328 None:intergenic
AAACATCACAAGTGCCTCCA+AGG 0.555823 2.3:+29922588 None:intergenic
ATAATTTAAGAGTACAAGAT+GGG 0.578232 2.3:-29921631 MS.gene77628:CDS
AGTACAAGATGGGAGCTACA+TGG 0.581291 2.3:-29921621 MS.gene77628:CDS
AACAAATGGGACCAAATCCA+AGG 0.586140 2.3:-29921707 MS.gene77628:CDS
GTGTTCCCTCATCCTCCTGA+AGG 0.587543 2.3:-29922151 MS.gene77628:intron
AAACGAAATGACATCCTTGG+AGG 0.589096 2.3:-29922602 None:intergenic
GCAGGATATCCAAACATGAA+AGG 0.592144 2.3:-29921995 MS.gene77628:CDS
TACTAGCAAAAGAAATTGTG+AGG 0.592380 2.3:-29922456 MS.gene77628:CDS
TTGGTGTTTGGAAGAAAAGG+TGG 0.597185 2.3:-29921844 MS.gene77628:CDS
AATCAGGAGAGACCGTAAGT+AGG 0.608714 2.3:-29922510 MS.gene77628:CDS
AATATGTGGCATTCAAGATG+AGG 0.620299 2.3:-29921735 MS.gene77628:CDS
TCTGTGAAGTTAAAATCAGG+AGG 0.623384 2.3:+29922433 None:intergenic
TCGTACCTTCAGGAGGATGA+GGG 0.629341 2.3:+29922146 None:intergenic
TTGATCTTTAGTAGGAACGA+TGG 0.638791 2.3:+29922324 None:intergenic
AGAGATGGCAGTCAAGCACA+AGG 0.648134 2.3:-29921926 MS.gene77628:CDS
AGATTAATCGTACCTTCAGG+AGG 0.657477 2.3:+29922139 None:intergenic
GGATATCTATCACCATACAA+AGG 0.686019 2.3:-29921974 MS.gene77628:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATGTTCAAAATAAATT+TGG - chr2.3:29921619-29921638 MS.gene77628:CDS 15.0%
!! AAAGATCAAATTCGTTATAT+TGG - chr2.3:29921844-29921863 MS.gene77628:CDS 20.0%
!! CAAAATAAATTTGGAAAATC+AGG - chr2.3:29921628-29921647 MS.gene77628:CDS 20.0%
!! GTGATTTATATAGTATTACT+TGG - chr2.3:29922058-29922077 MS.gene77628:intron 20.0%
!!! ATAATTTAAGAGTACAAGAT+GGG - chr2.3:29922523-29922542 MS.gene77628:CDS 20.0%
!!! TATAATTTAAGAGTACAAGA+TGG - chr2.3:29922522-29922541 MS.gene77628:CDS 20.0%
! AATGTCATTGAAAGAACAAT+TGG - chr2.3:29922291-29922310 MS.gene77628:CDS 25.0%
! ATTTCTGTGAAGTTAAAATC+AGG + chr2.3:29921727-29921746 None:intergenic 25.0%
! TAACGAATTTGATCTTTAGT+AGG + chr2.3:29921841-29921860 None:intergenic 25.0%
! TCTTTCAATGACATTTCTAA+GGG + chr2.3:29922286-29922305 None:intergenic 25.0%
! TTCTTTCAATGACATTTCTA+AGG + chr2.3:29922287-29922306 None:intergenic 25.0%
!! ACACATTTTTCATTTCTTCA+AGG + chr2.3:29921987-29922006 None:intergenic 25.0%
!!! ATCTTTTCTTGTTTGATTAG+TGG + chr2.3:29922363-29922382 None:intergenic 25.0%
!!! ATTTCTAGGAAAGTATTACT+TGG - chr2.3:29922131-29922150 MS.gene77628:intron 25.0%
!!! TTAATCACTTTTGTTGTTGT+TGG - chr2.3:29921919-29921938 MS.gene77628:CDS 25.0%
AAAAGATTAATCGTACCTTC+AGG + chr2.3:29922021-29922040 None:intergenic 30.0%
AAGATGAGGAATTCAACAAA+TGG - chr2.3:29922433-29922452 MS.gene77628:CDS 30.0%
AGAAATTCCATCCAAAATCA+AGG - chr2.3:29921741-29921760 MS.gene77628:CDS 30.0%
AGATGAGGAATTCAACAAAT+GGG - chr2.3:29922434-29922453 MS.gene77628:CDS 30.0%
ATTCGTTATATTGGCAGAAA+AGG - chr2.3:29921853-29921872 MS.gene77628:CDS 30.0%
CATAACTTCATTCGAATATG+TGG - chr2.3:29922405-29922424 MS.gene77628:CDS 30.0%
GATAGATATCCTTTCATGTT+TGG + chr2.3:29922171-29922190 None:intergenic 30.0%
TACTAGCAAAAGAAATTGTG+AGG - chr2.3:29921698-29921717 MS.gene77628:CDS 30.0%
TGATATCTTTCACCTTTGTA+TGG + chr2.3:29922195-29922214 None:intergenic 30.0%
TTCACTAAACTTCCTACTTA+CGG + chr2.3:29921659-29921678 None:intergenic 30.0%
! TCAAGGATGATAGAAGATTT+TGG - chr2.3:29921758-29921777 MS.gene77628:CDS 30.0%
! TCTTCTATCATCCTTGATTT+TGG + chr2.3:29921755-29921774 None:intergenic 30.0%
! TCTTGTTTGATTAGTGGAAA+TGG + chr2.3:29922357-29922376 None:intergenic 30.0%
! TTGAAAGAACAATTGGTGTT+TGG - chr2.3:29922298-29922317 MS.gene77628:CDS 30.0%
!! TTTGTTTTCCAACAACTTAG+TGG + chr2.3:29922580-29922599 None:intergenic 30.0%
!!! AGATTTTGGCCTTATTTTGA+TGG - chr2.3:29921772-29921791 MS.gene77628:CDS 30.0%
AATATGTGGCATTCAAGATG+AGG - chr2.3:29922419-29922438 MS.gene77628:CDS 35.0%
GGATATCTATCACCATACAA+AGG - chr2.3:29922180-29922199 MS.gene77628:CDS 35.0%
TCAAATTGCCACTAAGTTGT+TGG - chr2.3:29922569-29922588 MS.gene77628:CDS 35.0%
TCTGTGAAGTTAAAATCAGG+AGG + chr2.3:29921724-29921743 None:intergenic 35.0%
TTGATCTTTAGTAGGAACGA+TGG + chr2.3:29921833-29921852 None:intergenic 35.0%
! AAGTATTACTTGGTTGATGC+AGG - chr2.3:29922141-29922160 MS.gene77628:intron 35.0%
! ACTAACATGACATTTTGCGT+TGG + chr2.3:29921883-29921902 None:intergenic 35.0%
! CAATTGGTGTTTGGAAGAAA+AGG - chr2.3:29922307-29922326 MS.gene77628:CDS 35.0%
! CTATCATCCTTGATTTTGGA+TGG + chr2.3:29921751-29921770 None:intergenic 35.0%
!! CACATTCCTGATTTTAGAGA+TGG - chr2.3:29922213-29922232 MS.gene77628:CDS 35.0%
!!! CCTTATTTTGATGGATGCAT+CGG - chr2.3:29921781-29921800 MS.gene77628:CDS 35.0%
AACAAATGGGACCAAATCCA+AGG - chr2.3:29922447-29922466 MS.gene77628:CDS 40.0%
AGATTAATCGTACCTTCAGG+AGG + chr2.3:29922018-29922037 None:intergenic 40.0%
AGGCACTTGTGATGTTTCTT+TGG - chr2.3:29921572-29921591 MS.gene77628:CDS 40.0%
CCGATGCATCCATCAAAATA+AGG + chr2.3:29921784-29921803 None:intergenic 40.0%
CGAGCATATATCCTTGGATT+TGG + chr2.3:29922461-29922480 None:intergenic 40.0%
GCAGGATATCCAAACATGAA+AGG - chr2.3:29922159-29922178 MS.gene77628:CDS 40.0%
! TTGGTGTTTGGAAGAAAAGG+TGG - chr2.3:29922310-29922329 MS.gene77628:CDS 40.0%
!! TGACTGCCATCTCTAAAATC+AGG + chr2.3:29922222-29922241 None:intergenic 40.0%
!!! TCACTTTTGTTGTTGTTGGC+TGG - chr2.3:29921923-29921942 MS.gene77628:CDS 40.0%
AAACATCACAAGTGCCTCCA+AGG + chr2.3:29921569-29921588 None:intergenic 45.0%
AATCAGGAGAGACCGTAAGT+AGG - chr2.3:29921644-29921663 MS.gene77628:CDS 45.0%
AGTACAAGATGGGAGCTACA+TGG - chr2.3:29922533-29922552 MS.gene77628:CDS 45.0%
CTCGTTCGAGCATATATCCT+TGG + chr2.3:29922467-29922486 None:intergenic 45.0%
TCTTTAGTAGGAACGATGGC+AGG + chr2.3:29921829-29921848 None:intergenic 45.0%
!!! TTTTATTTTTATATATTTCT+AGG - chr2.3:29922117-29922136 MS.gene77628:intron 5.0%
AGAGATGGCAGTCAAGCACA+AGG - chr2.3:29922228-29922247 MS.gene77628:CDS 50.0%
ATCGTACCTTCAGGAGGATG+AGG + chr2.3:29922012-29922031 None:intergenic 50.0%
TCGTACCTTCAGGAGGATGA+GGG + chr2.3:29922011-29922030 None:intergenic 50.0%
!! GGATGCATCGGTGCTATAGA+TGG - chr2.3:29921793-29921812 MS.gene77628:CDS 50.0%
!! TTTGTTGTTGTTGGCTGGCC+TGG - chr2.3:29921928-29921947 MS.gene77628:CDS 50.0%
GTGTTCCCTCATCCTCCTGA+AGG - chr2.3:29922003-29922022 MS.gene77628:CDS 55.0%
CGTGTGTCATGCGCAGTACC+AGG + chr2.3:29921949-29921968 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 29921559 29922617 29921559 ID=MS.gene77628
chr2.3 mRNA 29921559 29922617 29921559 ID=MS.gene77628.t1;Parent=MS.gene77628
chr2.3 exon 29922152 29922617 29922152 ID=MS.gene77628.t1.exon1;Parent=MS.gene77628.t1
chr2.3 CDS 29922152 29922617 29922152 ID=cds.MS.gene77628.t1;Parent=MS.gene77628.t1
chr2.3 exon 29921559 29922037 29921559 ID=MS.gene77628.t1.exon2;Parent=MS.gene77628.t1
chr2.3 CDS 29921559 29922037 29921559 ID=cds.MS.gene77628.t1;Parent=MS.gene77628.t1
Gene Sequence

>MS.gene77628

ATGACATCCTTGGAGGCACTTGTGATGTTTCTTTGGAGTTATGCGCATAGCGAGACTAATAGAAATGTTCAAAATAAATTTGGAAAATCAGGAGAGACCGTAAGTAGGAAGTTTAGTGAAGTTTTAGAAAGTTTATGTTTACTAGCAAAAGAAATTGTGAGGCCTCCTGATTTTAACTTCACAGAAATTCCATCCAAAATCAAGGATGATAGAAGATTTTGGCCTTATTTTGATGGATGCATCGGTGCTATAGATGGAACGCATATTCCTGCCATCGTTCCTACTAAAGATCAAATTCGTTATATTGGCAGAAAAGGATATCCAACGCAAAATGTCATGTTAGTCTGTAACTTAGACATGTTAATCACTTTTGTTGTTGTTGGCTGGCCTGGTACTGCGCATGACACACGTATTCTTACGTCAGTCCTTGAAGAAATGAAAAATGTGTTCCCTCATCCTCCTGAAGGTACGATTAATCTTTTTTTTATAACTAAAATTTGTGATTTATATAGTATTACTTGGAAACAATGATTTTTTATTTTAACAATGATTTTTTTATTTTATTTTTATATATTTCTAGGAAAGTATTACTTGGTTGATGCAGGATATCCAAACATGAAAGGATATCTATCACCATACAAAGGTGAAAGATATCACATTCCTGATTTTAGAGATGGCAGTCAAGCACAAGGCATTCGTGAAATATTCAATCATGCACATTCATCCCTTAGAAATGTCATTGAAAGAACAATTGGTGTTTGGAAGAAAAGGTGGCATATTTTATGTGATATGAGACCATTTCCACTAATCAAACAAGAAAAGATCATAGTTGCAACAACAACACTTCATAACTTCATTCGAATATGTGGCATTCAAGATGAGGAATTCAACAAATGGGACCAAATCCAAGGATATATGCTCGAACGAGAAGAAGAAAGAAACACTACTGAAGATTCGAGTTCATATAATTTAAGAGTACAAGATGGGAGCTACATGGATAGAGCTAGAAATCAAATTGCCACTAAGTTGTTGGAAAACAAAAATCGTTCAAGTTTATGA
Protein sequence

>MS.gene77628.t1

MTSLEALVMFLWSYAHSETNRNVQNKFGKSGETVSRKFSEVLESLCLLAKEIVRPPDFNFTEIPSKIKDDRRFWPYFDGCIGAIDGTHIPAIVPTKDQIRYIGRKGYPTQNVMLVCNLDMLITFVVVGWPGTAHDTRILTSVLEEMKNVFPHPPEGKYYLVDAGYPNMKGYLSPYKGERYHIPDFRDGSQAQGIREIFNHAHSSLRNVIERTIGVWKKRWHILCDMRPFPLIKQEKIIVATTTLHNFIRICGIQDEEFNKWDQIQGYMLEREEERNTTEDSSSYNLRVQDGSYMDRARNQIATKLLENKNRSSL